SMTL ID : 1l3v.1

Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 15 base pairs of duplex DNA following addition of dTTP, dATP, dCTP, and dGTP residues.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 11 residues within 4Å: Chain C: E.29, N.30, Y.31, D.76, R.79, L.99, D.112, I.309, N.311, A.313, T.323 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.79, C:D.112, C:N.311, C:N.311, C:A.313, C:R.79 Water bridges: C:D.76, C:R.79, C:Q.312, C:E.29, C:E.29 GLC-FRU.2: 6 residues within 4Å: Chain C: E.455, V.458, Q.459, K.462, R.488, E.492 5 PLIP interactions: 5 interactions with chain C Water bridges: C:E.455, C:Q.459, C:E.492, C:E.492, C:R.488, C:R.488 Hydrogen bonds: C:Q.459, C:K.462, C:E.492

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain C: H.386, R.406, K.410 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Q.360 Salt bridges: C:R.406, C:K.410 SO4.4: 1 residues within 4Å: Chain C: R.523 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.523, C:R.523 Salt bridges: C:R.523 SO4.5: 3 residues within 4Å: Chain C: M.3, A.4, R.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.4 Salt bridges: C:R.47

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain C: D.357, Y.358, D.534 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.357, C:Y.358, C:D.534

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, S.J. et al., Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2003-03-25

Peptides

DNA Polymerase I: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA Polymerase I

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